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@Article{Chapman2006,
  Title                    = {Letting the gene out of the bottle: the population genetics of genetically modified crops},
  Author                   = {Mark A. Chapman and
 John M. Burke},
  Journal                  = {The New Pythologist},
  Year                     = {2006},

  Month                    = {May},
  Number                   = {3},
  Pages                    = {429--443},
  Volume                   = {170},

  Abstract                 = {Genetically modified (GM) plants are rapidly becoming a common feature of modern agriculture. This transition to engineered crops has been driven by a variety of potential benefits, both economic and ecological. The increase in the use of GM crops has, however, been accompanied by growing concerns regarding their potential impact on the environment. Here, we focus on the escape of transgenes from cultivation via crop x wild hybridization. We begin by reviewing the literature on natural hybridization, with particular reference to gene flow between crop plants and their wild relatives. We further show that natural selection, and not the overall rate of gene flow, is the most important factor governing the spread of favorable alleles. Hence, much of this review focuses on the likely effects of transgenes once they escape. Finally, we consider strategies for transgene containment.},
  Doi                      = {10.1111/j.1469-8137.2006.01710.x},
  File                     = {:Chapman_et_al-2006-New_Phytologist.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Contreras1991,
  Title                    = {Conditional-Suicide Containment System for Bacteria Which Mineralize Aromatics},
  Author                   = {Asunción Contreras and
Soren Molin and
Juan-Luis Ramos},
  Journal                  = {Applied and Environmental Microbiology},
  Year                     = {1991},
  Number                   = {4},
  Pages                    = {1504--1508},
  Volume                   = {57},

  Abstract                 = {A model conditional-suicide system to control genetically engineered microorganisms able to degrade substituted benzoates is reported. The system is based on two elements. One element consists of a fusion between the promoter of the Pseudomonas putida TOL plasmid-encoded meta-cleavage pathway operon (Pm) and the lacI gene encoding Lac repressor plus xylS, coding for the positive regulator of Pm. The other element carries a fusion between the Ptac promoter and the gef gene, which encodes a killing function. In the presence of XylS effectors, LacI protein is synthesized, preventing the expression of the killing function. In the absence of effectors, expression of the Ptac::gef cassette is no longer prevented and a high rate of cell killing is observed. The substitution of XylS for XylSthr45, a mutant regulator with altered effector specificity and increased affinity for benzoates, allows the control of populations able to degrade a wider range of benzoates at micromolar substrate concentrations. Given the wide effector specificity of the key regulators, the wild-type and mutant XylS proteins, the system should allow the control of populations able to metabolize benzoate; methyl-, dimethyl-, chloro-, dichloro-, ethyl-, and methoxybenzoates; salicylate; and methyl- and chlorosalicylates. A small population of genetically engineered microorganisms became Gef resistant; however, the mechanism of such survival remains unknown.},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Friedl2009,
  Title                    = {Synthetic Gene Networks That Count},
  Author                   = {Ari E. Friedland and
Timothy K. Lu and
 Xiao Wang and
David Shi and
George Church and
James J. Collins},
  Journal                  = {Science},
  Year                     = {2009},

  Month                    = {May},
  Number                   = {5931},
  Pages                    = {1199--1202},
  Volume                   = {324},

  __markedentry            = {[lukas:3]},
  Doi                      = {10.1126/science.1172005},
  File                     = {:Science-2009-Smolke-1156-7.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Gallagher2015,
  Title                    = {Multilayered genetic safeguards limit growth of microorganisms to defined environments},
  Author                   = {Ryan R. Gallagher and
Jaymin R. Patel and
Alexander L. Interiano1 and
Alexis J. Rovner and
Farren J. Isaacs},
  Journal                  = {Nucleic Acids Research},
  Year                     = {2015},

  Month                    = {Feb},
  Number                   = {3},
  Pages                    = {1945--1954},
  Volume                   = {43},

  __markedentry            = {[lukas:3]},
  Abstract                 = {Genetically modified organisms (GMOs) are commonly used to produce valuable compounds in closed industrial systems. However, their emerging applications in open clinical or environmental settings require enhanced safety and security measures. Intrinsic biocontainment, the creation of bacterial hosts unable to survive in natural environments, remains a major unsolved biosafety problem. We developed a new biocontainment strategy containing overlapping 'safeguards'-engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome-to restrict viability of Escherichia coli cells to media containing exogenously supplied synthetic small molecules. These multilayered safeguards maintain robust growth in permissive conditions, eliminate persistence and limit escape frequencies to <1.3 × 10(-12). The staged approach to safeguard implementation revealed mechanisms of escape and enabled strategies to overcome them. Our safeguarding strategy is modular and employs conserved mechanisms that could be extended to clinically or industrially relevant organisms and undomesticated species.},
  Doi                      = {10.1093/nar/gku1378},
  File                     = {:Nucl. Acids Res.-2015-Gallagher-1945-54.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Halford2000,
  Title                    = {Genetically modified crops: methodology, benefits, regulation and public concerns},
  Author                   = {Nigel G. Halford and
 Peter R. Shewry},
  Journal                  = {British Medical Bulletin},
  Year                     = {2000},
  Number                   = {1},
  Pages                    = {62--73},
  Volume                   = {56},

  __markedentry            = {[lukas:3]},
  Abstract                 = {The genetic modification of crop plants from the methodology involved in their production through to the current debate on their use in agriculture are reviewed. Techniques for plant transformation by Agrobacterium tumefaciens and particle bombardment, and for the selection of transgenic plants using marker genes are described. The benefits of currently available genetically modified (GM) crops in reducing waste and agrochemical use in agriculture, and the potential of the technology for further crop improvement in the future are discussed. The legal requirements for containment of novel GM crops and the roles of relevant regulatory bodies in ensuring that GM crops and food are safe are summarized. Some of the major concerns of the general public regarding GM crops and food: segregation of GM and non-GM crops and cross-pollination between GM crops and wild species, the use of antibiotic resistance marker genes, the prevention of new allergens being introduced in to the food chain and the relative safety of GM and non-GM foods are considered. Finally, the current debate on the use of GM crops in agriculture and the need for the government, scientists and industry to persevere with the technology in the face of widespread hostility is studied.},
  Doi                      = {10.1258/0007142001902978},
  File                     = {:Br Med Bull-2000-Halford-62-73.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Hu2007,
  Title                    = {Progress in the evaluation of transgenic fish for possible ecological risk and its containment strategies.},
  Author                   = {Wei Hu and
YaPing Wang and
ZuoYan Zhu},
  Journal                  = {Science in China, Series C: Life Sciences},
  Year                     = {2007},

  Month                    = {Oct},
  Note                     = {Not available via UB HD},
  Number                   = {5},
  Pages                    = {573--579},
  Volume                   = {55},

  __markedentry            = {[lukas:1]},
  Abstract                 = {Genetically improved transgenic fish possess many beneficial economic traits; however, the commercial aquaculture of transgenic fish has not been performed till date. One of the major reasons for this is the possible ecological risk associated with the escape or release of the transgenic fish. Using a growth hormone transgenic fish with rapid growth characteristics as a subject, this paper analyzes the following: the essence of the potential ecological risks posed by transgenic fish; ecological risk in the current situation due to transgenic fish via one-factor phenotypic and fitness analysis, and mathematical model deduction. Then, it expounds new ideas and the latest findings using an artificially simulated ecosystem for the evaluation of the ecological risks posed by transgenic fish. Further, the study comments on the strategies and principles of controlling these ecological risks by using a triploid approach. Based on these results, we propose that ecological risk evaluation and prevention strategies are indispensable important components and should be accompanied with breeding research in order to provide enlightments for transgenic fish breeding, evaluation of the ecological risks posed by transgenic fish, and development of containment strategies against the risks.},
  Doi                      = {10.1007/s11427-007-0089-y},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Huesken2010,
  Title                    = {Evaluating biological containment strategies for pollen-mediated gene flow},
  Author                   = {Alexandra Hüsken and
Sabine Prescher and
Joachim Schieman},
  Journal                  = {Environmental Biosafety Research},
  Year                     = {2010},

  Month                    = {Dec},
  Number                   = {2},
  Pages                    = {67--73},
  Volume                   = {9},

  __markedentry            = {[lukas:3]},
  Abstract                 = {Several biological containment methods have been developed to reduce pollen dispersal; many of them only have a proof of concept in a model plant species. This review focuses on biological containment measures which were tested for their long-term efficiency at the greenhouse or field scale level, i.e. plastid transformation, transgene excission, cleistogamy and cytoplasmic male sterility (CMS). Pollen-mediated gene transfer in transplastomic tobacco could occur at very low frequencies if the predominant mode of inheritance is maternal. Transgene excision from tobacco pollen can be made highly efficient by coexpression of two recombinases. For cleistogamous oilseed rape it was shown that some flowers were partially open depending on genotypes, environment and recording dates. Reports on the stability of CMS in maize and sunflower indicated that there is a high variability for different genotypes under different environmental conditions and over successive years. But for both crop types some stable lines could be selected. These data demonstrate that the biological containment methods discussed are very promising for reducing gene flow but that no single containment strategy provides 100% reduction. However, the necessary efficiency of biological containment methods depends on the level of containment required. The containment level may need to be higher for safety purposes (e.g. production of special plant-made pharmaceuticals), while much lower containment levels may already be sufficient to reach coexistence goals. It is concluded that where pollen-mediated gene flow must be prevented altogether, combinations of complementary containment systems will be required.},
  Doi                      = {10.1051/ebr/2010009},
  File                     = {:ebr1008.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Electronic{Kazantsevn.d.,
  Title                    = {X-ray Crystallography},
  Author                   = {Roman Kazantsev and
Michelle Towles},
  HowPublished             = {chemwiki.ucdavis.edu},
  Language                 = {English},
  Organization             = {UC Davis},
  Url                      = {http://chemwiki.ucdavis.edu/Analytical_Chemistry/Instrumental_Analysis/Diffraction/X-ray_Crystallography},
  Year                     = {n.d.},

  __markedentry            = {[lukas:2]},
  Abstract                 = {X-ray Crystallography is a scientific method used to determine the arrangement of atoms of a crystalline solid in three dimensional space. This technique takes advantage of the interatomic spacing of most crystalline solids by employing them as a diffraction gradient for x-ray light, which has wavelengths on the order of 1 angstrom (10^-8 cm).},
  Owner                    = {lukas},
  Timestamp                = {2015.03.25}
}

@Article{Knudsen1995,
  Title                    = {Development and testing of improved suicide functions for biological containment of bacteria},
  Author                   = {S. Knudsen and
P. Saadbye and
L.H.  Hansen and
A. Collier and 
B. L. Jacobsen and
J. Schlundt and
O. H. Karlström},
  Journal                  = {Applied and Environmental Microbiology},
  Year                     = {1995},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {985--991},
  Volume                   = {61},

  __markedentry            = {[lukas:3]},
  Abstract                 = {We have developed very efficient suicide functions for biological containment based on the lethal Escherichia coli relF gene. The suicide functions are placed in duplicate within a plasmid and arranged to prevent inactivation by deletion, recombination, and insertional inactivation. The efficiency of this concept was tested in a plasmid containment system that prevents transfer of plasmids to wild-type bacteria. Protection against plasmid transfer was assayed in test tubes and in rat intestine. Protection was efficient and refractory to inactivation by mutation and transposons. The efficiency of the suicide system was also tested in soil and seawater. We show that unprecedented suicide efficiency can be achieved in soil and seawater after suicide induction by IPTG (isopropyl-beta-D-thiogalactopyranoside). More than 7 orders of magnitude reduction in suicide bacteria was achieved.},
  Doi                      = {0099-2240/95/$04.0010},
  File                     = {:610985.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Kristoffersen2000,
  Title                    = {Bacterial toxin-antitoxin gene system as containment control in yeast cells},
  Author                   = {P. Kristoffersen and
G.B. Jensen and
K. Gerdes and 
J. Piskur},
  Journal                  = {Applied and Environmental Microbiology},
  Year                     = {2000},

  Month                    = {Dec},
  Number                   = {12},
  Pages                    = {5524--5526},
  Volume                   = {66},

  __markedentry            = {[lukas:3]},
  Abstract                 = {The potential of a bacterial toxin-antitoxin gene system for use in containment control in eukaryotes was explored. The Escherichia coli relE and relB genes were expressed in the yeast Saccharomyces cerevisiae. Expression of the relE gene was highly toxic to yeast cells. However, expression of the relB gene counteracted the effect of relE to some extent, suggesting that toxin-antitoxin interaction also occurs in S. cerevisiae. Thus, bacterial toxin-antitoxin gene systems also have potential applications in the control of cell proliferation in eukaryotic cells, especially in those industrial fermentation processes in which the escape of genetically modified cells would be considered highly risky.},
  Doi                      = {0099-2240/00/$04.0010},
  File                     = {:am005524.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Lederberg1952,
  Title                    = {Replica plating and indirect Selection of Bacterial Mutants},
  Author                   = {Joshua Lederberg and
Esther M. Lederberg},
  Journal                  = {Journal of Bacteriology},
  Year                     = {1952},

  Month                    = {Mar},
  Number                   = {3},
  Pages                    = {399--406},
  Volume                   = {63},

  __markedentry            = {[lukas:1]},
  File                     = {:jbacter00003-0114.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.25}
}

@Article{Lee2012,
  Title                    = {Biocontainment strategies for live lactic acid bacteria vaccine vectors},
  Author                   = {Peter Lee},
  Journal                  = {Bioengineered Bugs},
  Year                     = {2012},

  Month                    = {Jan--Feb},
  Number                   = {1},
  Pages                    = {75-77},
  Volume                   = {1},

  __markedentry            = {[lukas:1]},
  Abstract                 = {Stability is an important issue when engineering bacteria for use as live vaccine vectors. For the majority of live bacterial vaccines, the antigen-encoding gene is either plasmid located or integrated into the chromosome. Regardless, several safety concerns can be raised for both instances. One concern when using plasmid-encoded antigens is the transfer of antibiotic resistance markers. Alternatively, for chromosomal integrated antigens however, the concern focuses on the spread and possible release of genetically-modified microorganisms (GMM) into the environment, which is problematic. Their recombinant nature calls for a proper bio-containment strategy to be implemented or in place before any realistic attempt at releasing a live bacterial vaccine. No examples of human bacterial vaccines causing problems among animals have been found in the literature but the possibility exists and has to be both tested and evaluated before release of a live bacterial vaccine. The ideal GMM for use in humans should therefore contain the minimal amount of foreign DNA and must not include an antibiotic resistance marker. Furthermore, the possibilities of transgene horizontal transfer must be minimized, and GMM lethality for biocontainment should be achieved in an unconfined environment.},
  Doi                      = {10.4161/bbug.1.1.10594},
  File                     = {:bbug0101_0075.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Li2013,
  Title                    = {A Built-In Strategy to Mitigate Transgene Spreading from Genetically Modified Corn},
  Author                   = {Jing Li and
Hui Yu and
Fengzhen Zhang and
Chaoyang Lin and
Jianhua Gao and
Jun Fang and
Xiahui Ding and
Zhicheng Shen and
Xiaoli Xu},
  Journal                  = {PLoS One},
  Year                     = {2013},

  Month                    = {Dec},
  Number                   = {12},
  Volume                   = {8},

  Abstract                 = {Transgene spreading is a major concern in cultivating genetically modified (GM) corn. Cross-pollination may cause the spread of transgenes from GM cornfields to conventional fields. Occasionally, seed lot contamination, volunteers, mixing during sowing, harvest, and trade can also lead to transgene escape. Obviously, new biological confinement technologies are highly desired to mitigate transgene spreading in addition to physical separation and isolation methods. In this study, we report the development of a built-in containment method to mitigate transgene spreading in corn. In this method, an RNAi cassette for suppressing the expression of the nicosulfuron detoxifying enzyme CYP81A9 and an expression cassette for the glyphosate tolerant 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene G10 were constructed and transformed into corn via Agrobacterium-mediated transformation. The GM corn plants that were generated were found to be sensitive to nicosulfuron but resistant to glyphosate, which is exactly the opposite of conventional corn. Field tests demonstrated that GM corn plants with silenced CYP81A9 could be killed by applying nicosulfuron at 40 g/ha, which is the recommended dose for weed control in cornfields. This study suggests that this built-in containment method for controlling the spread of corn transgenes is effective and easy to implement.},
  Doi                      = {10.1371/journal.pone.0081645},
  File                     = {:pone.0081645.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Li2009,
  Title                    = {A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required},
  Author                   = {Qin Li and
Yi-Jun Wu},
  Journal                  = {Applied Microbiology and Biotechnology},
  Year                     = {2009},

  Month                    = {Mar},
  Number                   = {4},
  Pages                    = {749--756},
  Volume                   = {82},

  __markedentry            = {[lukas:3]},
  Doi                      = {10.1007/s00253-009-1857-3},
  File                     = {:art%3A10.1007%2Fs00253-009-1857-3.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Lu2009,
  Title                    = {Next-generation synthethic gene networks},
  Author                   = {Timothy K. Lu and
Ahmad S. Khalil and
James J. Collins},
  Journal                  = {Nature Biotechnology},
  Year                     = {2009},

  Month                    = {Dec},
  Pages                    = {1139--1150},
  Volume                   = {27},

  __markedentry            = {[lukas:3]},
  Doi                      = {10.1038/nbt.1591},
  File                     = {:nbt.1591.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Mandell2015,
  Title                    = {Biocontainment of genetically modified organisms by synthetic protein design.},
  Author                   = {Daniel J. Mandell and
Marc J. Lajoie and
Michael T. Mee and
Ryo Takeuchi and
Gleb Kuznetsov and
Julie E. Norville and
Christopher J. Gregg and
Barry L. Stoddard and
George M. Church},
  Journal                  = {Nature},
  Year                     = {2015},
  Number                   = {7537},
  Pages                    = {55--60},
  Volume                   = {518},

  __markedentry            = {[lukas:5]},
  Abstract                 = {Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.},
  Doi                      = {10.1038/nature14121},
  File                     = {:gmocontainment.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.17}
}

@Article{Moe-Behrens2013,
  Title                    = {Preparing synthetic biology for the world},
  Author                   = {Gerd H. G. Moe-Behrens and
Rene Davis and
Karmella A. Haynes},
  Journal                  = {Frontiers in Microbiology},
  Year                     = {2013},

  Month                    = {Jan},
  Number                   = {5},
  Volume                   = {4},

  __markedentry            = {[lukas:1]},
  Abstract                 = {Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or "living devices." As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.},
  Doi                      = {10.3389/fmicb.2013.00005},
  File                     = {:fmicb-04-00005.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Molin1993,
  Title                    = {Suicidal Genetic Elements and their use in biological containment of bacteria},
  Author                   = {S. Molin and
L. Boe and
L. B. Jensen and
C. S. Kristensen and
M. Givskov and
J. L. Ramos and
A. K. Bej},
  Journal                  = {Annual Review of Microbiology},
  Year                     = {1993},
  Pages                    = {139--166},
  Volume                   = {47},

  __markedentry            = {[lukas:3]},
  Abstract                 = {The potential risks of unintentional releases of genetically modified organisms, and the lack of predictable behavior of these in the environment, are the subject of considerable concern. This concern is accentuated in connection with the next phase of gene technology comprising deliberate releases. The possibilities of reducing such potential risks and increasing the predictability of the organisms are discussed for genetically engineered bacteria. Different approaches towards designing disabled strains without seriously reducing their beneficial effects are presented. Principally two types of strain design are discussed: actively contained bacteria based on the introduction of controlled suicide systems, and passively contained strains based on genetic interference with their survival under environmental-stress conditions.},
  Doi                      = {10.1146/annurev.mi.47.100193.001035},
  File                     = {:annurev%2Emi%2E47%2E100193%2E001035.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Molin1987,
  Title                    = {Conditional Suicide System for Containment of Bacteria and Plasmids},
  Author                   = {S. Molin and
P. Klemm and
L. K. Poulsen and
H. Biel and
K. Gerdes and
P. Andersson},
  Journal                  = {Nature Biotechnology},
  Year                     = {1987},
  Pages                    = {1315--1318},
  Volume                   = {5},

  __markedentry            = {[lukas:3]},
  Doi                      = {10.1038/nbt1287-1315},
  File                     = {:nbt1287-1315.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Moon2010,
  Title                    = {Keeping the genie in the bottle: transgene biocontainment by excision in pollen},
  Author                   = {Hong S. Moon and
Yi Li and
C. Neal Stewart Jr},
  Journal                  = {Trends in Biotechnology},
  Year                     = {2010},

  Month                    = {Jan},
  Number                   = {1},
  Pages                    = {3--8},
  Volume                   = {28},

  Abstract                 = {Gene flow from transgenic plants is an environmental and regulatory concern. While biocontainment might be achieved using male sterility or transgenic mitigation tools, we believe that perhaps the optimal solution might be simply to remove transgenes from pollen. Male sterility might not be ideal for many pollinators, and might not be implementable using standardized genes. Transgenic mitigation might not be useful to control conspecific gene flow (e.g. crop to crop), and relies on competition and not biocontainment per se. Site-specific recombination systems could allow highly efficient excision of transgenes in pollen to eliminate, or at least minimize, unwanted transgene movement via pollen dispersal. There are other potential biotechnologies, such as zinc finger nucleases, that could be also used for transgene excision.},
  Doi                      = {10.1016/j.tibtech.2009.09.008},
  File                     = {:1-s2.0-S0167779909001826-main.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Murphy2007,
  Title                    = {Improving containment strategies in biopharming},
  Author                   = {Denis J. Murphy},
  Journal                  = {Plant Biotechnology Journal},
  Year                     = {2007},

  Month                    = {Sep},
  Number                   = {5},
  Pages                    = {555-569},
  Volume                   = {5},

  Abstract                 = {This review examines the challenges of segregating biopharmed crops expressing pharmaceutical or veterinary agents from mainstream crops, particularly those destined for food or feed use. The strategy of using major food crops as production vehicles for the expression of pharmaceutical or veterinary agents is critically analysed in the light of several recent episodes of contamination of the human food chain by non-approved crop varieties. Commercially viable strategies to limit or avoid biopharming intrusion into the human food chain require the more rigorous segregation of food and non-food varieties of the same crop species via a range of either physical or biological methods. Even more secure segregation is possible by the use of non-food crops, non-crop plants or in vitro plant cultures as production platforms for biopharming. Such platforms already under development range from outdoor-grown Nicotiana spp. to glasshouse-grown Arabidopsis, lotus and moss. Amongst the more effective methods for biocontainment are the plastid expression of transgenes, inducible and transient expression systems, and physical containment of plants or cell cultures. In the current atmosphere of heightened concerns over food safety and biosecurity, the future of biopharming may be largely determined by the extent to which the sector is able to maintain public confidence via a more considered approach to containment and security of its plant production systems.},
  Doi                      = {10.1111/j.1467-7652.2007.00278.x},
  File                     = {:Murphy-2007-Plant_Biotechnology_Journal.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.21}
}

@Article{Pasotti2011,
  Title                    = {Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins release},
  Author                   = {L. Pasotti and
S. Zucca and
M. Lupotto and
M. G. Cusella De Angelis and
P. Magni},
  Journal                  = {Journal of Biological Engineering},
  Year                     = {2011},

  Month                    = {Jun},
  Number                   = {8},
  Volume                   = {5},

  Abstract                 = {BACKGROUND:
Bacterial cell lysis is a widely studied mechanism that can be achieved through the intracellular expression of phage native lytic proteins. This mechanism can be exploited for programmed cell death and for gentle cell disruption to release recombinant proteins when in vivo secretion is not feasible. Several genetic parts for cell lysis have been developed and their quantitative characterization is an essential step to enable the engineering of synthetic lytic systems with predictable behavior.

RESULTS:
Here, a BioBrick™ lysis device present in the Registry of Standard Biological Parts has been quantitatively characterized. Its activity has been measured in E. coli by assembling the device under the control of a well characterized N-3-oxohexanoyl-L-homoserine lactone (HSL) -inducible promoter and the transfer function, lysis dynamics, protein release capability and genotypic and phenotypic stability of the device have been evaluated. Finally, its modularity was tested by assembling the device to a different inducible promoter, which can be triggered by heat induction.

CONCLUSIONS:
The studied device is suitable for recombinant protein release as 96% of the total amount of the intracellular proteins was successfully released into the medium. Furthermore, it has been shown that the device can be assembled to different input devices to trigger cell lysis in response to a user-defined signal. For this reason, this lysis device can be a useful tool for the rational design and construction of complex synthetic biological systems composed by biological parts with known and well characterized function. Conversely, the onset of mutants makes this device unsuitable for the programmed cell death of a bacterial population.},
  Doi                      = {10.1186/1754-1611-5-8.},
  File                     = {:1754-1611-5-8.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

@Article{Pieper2000,
  Title                    = {Engineering bacteria for bioremediation},
  Author                   = {D. H. Pieper and
W. Reineke},
  Journal                  = {Current Opinion in Biotechnology},
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  __markedentry            = {[lukas:1]},
  Abstract                 = {The treatment of environmental pollution by microorganisms is a promising technology. Various genetic approaches have been developed and used to optimize the enzymes, metabolic pathways and organisms relevant for biodegradation. New information on the metabolic routes and bottlenecks of degradation is still accumulating, enlarging the available toolbox. With molecular methods allowing the characterization of microbial community structure and activities, the performance of microorganisms under in situ conditions and in concert with the indigenous microflora will become predictable.},
  Doi                      = {10.5772/19546},
  File                     = {:1-s2.0-S095816690000094X-main.pdf:PDF},
  Owner                    = {lukas},
  Timestamp                = {2015.03.28}
}

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  __markedentry            = {[lukas:2]},
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  Owner                    = {lukas},
  Timestamp                = {2015.03.25}
}

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  Title                    = {Mass Spectrometry},
  Author                   = {William Reusch},
  HowPublished             = {\url{http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/MassSpec/masspec1.htm}},
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  __markedentry            = {[lukas:2]},
  Owner                    = {lukas},
  Timestamp                = {2015.03.25}
}

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Adrian D. Haimovich and
Spencer R. Katz and
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  Journal                  = {Nature},
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@Article{Steidler2003,
  Title                    = {Genetically engineered probiotics},
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  Month                    = {Oct},
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  Title                    = {Programming cells by multiplex genome engineering and accelerated evolution},
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Mihails Delmans and
Guy-Bart Stan and
Tom Ellis},
  Publisher                  = {ACS Synthetic Biology},
  Year                     = {2015},
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